2C5S

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.8pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.857

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.047α = 90
b = 81.047β = 90
c = 140.893γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.00798, 0.97788, 0.97788, 0.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.52596.10.07522.78.518357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.57820.571.95.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.524.911724091598.90.2290.2270.278RANDOM58.61
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.481.242.48-3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_3_deg16.835
r_dihedral_angle_4_deg16.51
r_dihedral_angle_1_deg5.824
r_scangle_it4.586
r_scbond_it2.954
r_mcangle_it1.225
r_angle_refined_deg1.191
r_mcbond_it0.716
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_3_deg16.835
r_dihedral_angle_4_deg16.51
r_dihedral_angle_1_deg5.824
r_scangle_it4.586
r_scbond_it2.954
r_mcangle_it1.225
r_angle_refined_deg1.191
r_mcbond_it0.716
r_nbtor_refined0.306
r_symmetry_hbond_refined0.214
r_nbd_refined0.201
r_symmetry_vdw_refined0.164
r_xyhbond_nbd_refined0.132
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2964
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling